IIRC Mr Cruise had trouble keeping his lunch down when they took him up in an F-14 for real.
So the decision was made to back project all close ups.
Unlike the Froggies when they made Le Chevaliers du Ciel.
http://www.imdb.com/title/tt0092099/trivia
In preparation for his role, Tom Cruise was allowed to take 3 rides in the F-14 Tomcat. He vomited during the first trip but was okay during the other two.
Anthony Edwards is the only actor who didn't vomit while in the fighter jets.
Go the Goose-man.
Obviously no-one told them about the little trick of switching to 100 per cent oxygen...